Nextflow kuberun Remote origin did not advertise Ref for branch

[tjdurant]

Bug report

Expected behavior and actual behavior

Running nextflow script from a private repository using the nextlfow kuberun command produces error:

❯ nextflow kuberun <url_to_repo> -hub gitlab -profile docker -r <commit_hash_123>
Pod started: gigantic-sanger
N E X T F L O W  ~  version 22.04.5
Pulling <repo> ...
Remote origin did not advertise Ref for branch refs/tags/v1.0.0~2. This Ref may not exist in the remote or may be hidden by permission settings.

However, when I run the same command but with nextflow run it works:

❯ nextflow run <url_to_repo> -hub gitlab -profile docker -r <commit_hash_123>
N E X T F L O W  ~  version 22.04.5
Pulling <repo> ...
 downloaded from <url_to_repo>
Launching `<url_to_repo>` [condescending_albattani] DSL1 - revision: <commit_hash_123> [<commit_tag>]
executor >  local (2)
[e5/0d82f5] process > lineage_call_clia (<spec_id>) [  0%] 0 of 2

Happy to provide additional information as needed.

Thanks T

Environment

• Nextflow version: version 22.04.5
• Java version: openjdk version "11.0.13" 2021-10-19
• Operating system: macOS
• Bash version: zsh 5.8 (x86_64-apple-darwin20.0)
• Container runtime - docker-desktop

[pditommaso]

The kuberun command is going to be deprecated. Consider using the new Wave and Fusion features that are a great and simpler alternative to kuberun https://github.com/seqeralabs/wave-showcase/tree/master/example8